OK, I know what's going on, but not necessarily why. In the jnati code,
there are a number of places where they create a properties object
(ResolvingProperties) by adding all of the current system properties:
runtime.putAll(System.getProperties()); On my Mac, this only gets two
properties. However, if I do the following instead:
for (String key: System.getProperties().stringPropertyNames()) {
runtime.put(key, System.getProperty(key));
}
Everything works and all of the properties are currently loaded. Also if
I do a System.getProperties().size() it returns 2, so something is
certainly messed up and it may be why the putAll fails. I've added a
workaround in my initialization code that simply does a setProperty on
each property. That seems to get the count right and everything works
after that...
Thanks for trying to help. Got no idea why my system properties are
getting messed up, but I've got things working, now.
-- scooter
On 12/17/2012 01:53 PM, John May wrote:
Hi Scooter,
Do you have build, I can test on another machine if you like?
Thanks,
J
On 17 Dec 2012, at 21:40, Scooter Morris <[email protected]
<mailto:[email protected]>> wrote:
Hi all,
Just a quick update... I checked and the user.home property is
correctly set both before and after the attempt to call jni-inchi.
-- scooter
On 12/17/2012 01:30 PM, Scooter Morris wrote:
Hi John,
Thanks for the reply...
On 12/17/2012 12:29 PM, John May wrote:
Hi Scooter,
I'm on OS X 10.8.2 and have no problems on either Apple's 1.6.0_37
or Oracle's Java 7. I can't give a definite answer but some
possible pointers:
- I haven't done any Cytoscape development but I heard that in
Cyctoscape 3 they were now using OSGi (which I also don't know
loads about). However, something like not having "user.home" set in
the system properties sounds very much like an OSGi problem. Try
printing the home in an isolated java class and again with the plugin.
I haven't ported chemViz to 3.0, yet, so this is definitely not an
OSGi issue.
System.out.println(System.getProperty("user.home"));
Yeah, I'll give that a try and see if something is clobbering the
system properties completely...
Nope, the user.home property is correctly set
Thanks!
-- scooter
It seems strange this would only happen on OS X but it may well be
the case. Bioclipse use OSGi so it might be worth asking them if
they have had any issues with JNI-InChI and OSGi.
- If you're really desperate you could complete the InChI source to
java byte code using /nestedvm/. JChemPaint needed to do this as
you can't use JNI in applets. Rich Apodaca has a post about it
here:
http://depth-first.com/articles/2007/12/03/from-c-source-code-to-platform-independent-executable-jarfile-using-nestedvm-to-build-jinchi/
Thanks,
J
On 17 Dec 2012, at 18:12, Scooter Morris <[email protected]
<mailto:[email protected]>> wrote:
Hi all,
I'm trying to release a new version of the Cytoscape plugin:
chemViz, and have run into a major issue with JNI-InChI on
MacOS-X. For some reason, on MacOSX the user.home property is
never initialized. As a result, whenever I try to create a
molecule from an InChI string, I get a failure:
java.lang.UnsatisfiedLinkError: Expecting an absolute path of
the library:
${user.home}/.jnati/repo/jniinchi/1.03_1/MAC-X86_64/JniInchi-1.03_1-MAC-X86_64
Has anyone seen this, and any suggestions on a workaround? I'm on
MacOS X 10.8.2 with Java version 1.6.0_37. Any help would be
greatly appreciated.
-- scooter
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